Tag: open science

The New England Journal of Medicine has just published four articles that comment on the issue of “open access”. I will list these four articles and briefly comment on the two papers which are critical of open access publishing.

This article discusses potential problems associated with open access publishing but also conflates the issue of open access with the issue of inadequate peer review, as can be seen in this excerpt:

Of course, the terms “international,” “scientific,” “peer-reviewed,” “journal,” “article,” “editor,” and “publisher” do not have copyrighted or patented definitions and can have varied meanings, especially in the Internet age. Must an article be different from a submitted paper? Isn’t everything published online automatically international? Is there anything wrong with a situation in which the editor and publisher are just one person who has set up a website where researchers can submit their papers and pay a fee to have them laid out in a professional way and made available to all interested parties? Isn’t it a good thing that this vast number of new publishers and journals will make it possible to get all research — whatever its quality level — into the public domain? Perhaps. But describing a simple online-posting service as “an international, scientific, peer-reviewed journal” leads authors and readers to believe that they are submitting to or reading something they aren’t.

One central flaw of this argument is that open access does not necessarily mean lack of peer review, as previously discussed.

The article by Martin Frank tries to make the case that “open access” publishing itself costs quite a bit of money and that these funds could be better used for research purposes. He distinguishes between “gold open access”, where published articles are immediately available upon publication to the general public without any fees for the readers and “green open access”, which gives free access to the public after an initial period of pay-for-access. With green open access, the publisher generates some revenue during this initial period, whereas in “gold open access” publishing, the researchers usually pay a fee that covers the publication charges so that readers do not have to pay anything.

One section of the article especially caught my eye:

…..assuming that all articles had to be published with gold open access, Harvard Medical School would have to pay $13.5 million (at $1,350 per article) to publish the 10,000 articles authored by its faculty in 2010 — considerably more than the $3.75 million that was in its serials-acquisition budget that year. Research-intensive institutions will thus bear the burden of funding free access to the research literature, subsidizing access for less-research-intensive institutions, including pharmaceutical companies.

This calculation assumes that current pay-for-access journals do not charge researchers for the publication of their articles. I have previously addressed this issue, citing a specific example which shows that pay-for-access journals often charge the researchers several hundred dollars to publish an article. If researchers use color figures, the charges can run up to $2000 or $3000 per manuscript. These author fees are in addition to the fees that publishers of pay-for-access journals charge the readers. Martin Frank’s calculation ignores the author fees that Harvard researchers might be currently paying to publish in pay-for-access journals.

He also mentions the pharmaceutical companies as potential beneficiaries but fails to include other important beneficiaries:

1) Members of the general public, whose taxes paid for most of the biomedical research conducted in the United States and who should thus have a right to access the results of this publicly funded research

2) Individuals in countries who cannot afford the fees to read papers published in pay-for-access journals.

I recently came across a rant that lamented the advent of digital publishing, open access publishing and self-publishing in science. The rant was published in the Huffington Post as a “digital” blog post (ah, the irony), entitled “50 Shades of Grey in Scientific Publication: How Digital Publishing Is Harming Science”. It was reminiscent of the rants that might have been uttered by calligraphers who were upset about the emergence of Gutenberg’s printing press or concerns of European aristocrats in the wake of the French Revolution about whether commoners could ever govern a country. Normally I ignore rants, but this one was written by Dr. Douglas Fields, an outstanding neuroscientist and an excellent writer, who also serves as the Chief of the Nervous System Development and Plasticity Section at the National Institute of Child Health and Human Development. It is very difficult to understand how someone who is such an eminent scientist and has an extensive experience with scientific publishing would make so many bizarre statements about open access publishing.

My initial reaction was that Dr. Fields wrote it as a satirical piece, mocking the opponents of open access publishing by listing phobias and biases of interest groups that are trying to prevent free public access to the results of scientific research. Upon further reading, I realized that perhaps Dr. Fields did consider the statements in his article to be a valid critique of open access publishing and that it therefore warrants a response to point out the errors. Dr. Björn Brembs has already written one excellent response, but I think the topic is rather important and would benefit from additional responses. My problem is figuring out how to respond to a rant that is rife with so many inaccurate statements and fallacies. I will first summarize three key flaws in Dr. Fields’ reasoning and then move on to giving specific examples.

The title of Dr. Fields’ article mentions “digital publishing”, but in the article itself, the issue of “digital publishing” is conflated with “open access publishing” and “self-publishing”, even though these are very distinct entities. Digital publishing refers to the medium of publishing, and can take the form of articles or E-books which are viewed online or downloaded. Most scientific articles that I now read have been published digitally. I am very happy about this development and I do not miss the days when I had to spend hours in the library, photo-copying hundreds of scientific articles from print journals, both wasting my time and helping commit arbocide. Some of my colleagues still like to read the paper copies of journals, but most of us prefer the convenience of being able to archive thousands of scientific articles on a single USB flash drive and not have to maneuver around large stacks of paper. When it comes to books (literary, philosophical or scientific), I feel a bit differently. I derive tactile pleasure from printed books and I still find it easier to thumb through a printed book than browse an E-book. I can sympathize with concerns regarding digital publishing of books. However, when it comes to scientific papers (the focus of Dr. Fields’ article), most scientists would agree that digital publishing has made it easier for them to stay abreast of scientific developments.

Open access publishing can be defined as the publication of articles that are freely available to everyone. Readers do not need to be affiliated with any specific organizations and they do not have to pay for reading the published material. Many digitally published articles are NOT open access. Some of the digitally published journals actually charge up to $30 for reading one article, if one does not have a personal or institutional subscription to the journal. Conversely, there are printed publications which are, in a certain sense, “open access”, such as free local newspapers or flyers with grocery coupons. Anybody can obtain these for free. These examples just highlight the difference between the medium of publishing (digital versus paper) and the access to the published material (pay-for-access versus open access).

The term self-publishing, or the more derogatory term “vanity publishing’, is used when an author pays a fee and is guaranteed publication of the manuscript. The item is published either in a paper format or a digital format, and the author does not require approval of editor or peer reviewers prior to the publication. Most papers in open access scientific journals that I have come across are NOT self-publications, because they do undergo a peer review and the editors ultimately decide whether or not the manuscript should be published.

2. Open access publishing and rigorous peer review

The second major flaw is that Dr. Fields assumes open access publishing somehow impairs the peer review process and results in the publications of papers without scientific rigor. Much of my own experience stems from the PLOS family of open access journals, which include PLOS One, PLOS Medicine and PLOS Biology. The PLOS journals are among the most widely read open access journals in biomedical research. The last time I was a peer reviewer for a PLOS One manuscript, I used the same standards to assess the validity and scientific rigor of the manuscript that I use for pay-for-access journals. The PLOS editor used my review and that of the other anonymous peer reviewers to reach a decision about the manuscript. The editor requested that the authors of the manuscript make significant scientific revisions based on our reviews, similar to what I have seen in other pay-for-access journals. I never got the impression that the open access nature of the journal in any way diminished the rigorous peer review process. Most of the academic editors and reviewers of the PLOS open access journals are scientists who also routinely review manuscripts for pay-for-access journals and I have never heard of any reviewer having separate scientific review standards for open access papers. The PLOS editorial board members, that I have spoken to, have never experienced any pressure to publish a paper that was considered to be of poor scientific quality.

There are differences in terms of the criteria regarding novelty of the scientific papers that editors of open access journals may use to decide whether or not a manuscript is suitable for their journal. PLOS Medicine, PLOS Biology and the new open access journal eLife want to primarily publish ground-breaking, high-impact papers. Significant novelty and broad impact on the field of science have to be paired with high scientific rigor for these journals to consider a manuscript for publication. PLOS One, on the other hand, is more likely to publish papers that will not have such a broad impact on science, but it still requires scientific rigor and validity of the conclusions. This hierarchy of impact is not unique to open access journals. The pay-for-access journals Nature and Science also only consider manuscripts with a potentially high impact, whereas there are many other traditional pay-for-access journals that are willing to consider lower impact research findings as long as they demonstrate scientific rigor during the peer review process.

3. Open access publishing and corporate interests

The third major flaw in the article is that Dr. Fields assumes open access publishing somehow plays into the hands of capitalist corporate interests. Since open access publishing does not generate any revenue from its readers, it requires authors of manuscripts to pay for the publication costs. This might be an incentive for open access publishers to publish large numbers sub-standard scientific papers, because this way they could collect the authors’ publication fees. This is a valid concern and many of my colleagues who support open access publishing are aware of this potential conflict of interest. My response is that the reputation of an open access journal would suffer if it were to publish sub-standard scientific papers. This would lead to the loss of readers as well as submissions from authors, which would not want their work to appear in a disreputable journal. Furthermore, the peer review process of open access journals provides the necessary checks and balances to prevent publication of shoddy science. It is true that open access digital publishers could decide to increase the total number of published papers per year from say 10,000 to 100,000 in order to make more money. However, the decision about the scientific validity of a paper rests with the scientific editors and not with the publishers, so increasing the total number of available publication slots should not result in the publication of poor quality science as long as the peer review process remains rigorous and independent.

One has to also look at Dr. Fields’ concerns in the context of the current pay-for-access publishing industry, which is actually run by large corporations that reap huge profits from subscription fees. One of the largest academic publishers is Elsevier, which had over 3 billion US$ in revenues and an astonishing profit margin of 37% in 2011. The truth of the matter is that the current pay-for-access model is catering to corporate greed and is impairing the free sharing of scientific results. In addition to generating revenue from subscription fees, current pay-for-access publishers often also charge fees to the authors of the manuscripts. This may explain the high profit margin. I will elucidate this using the example of the journal Blood, one of the leading pay-for-access journals in hematology and vascular biology (which happens to be my area of interest). A review of the publication costs for Blood reveals that this journal charges $62 per printed page and $620 for each color figure, as well as $105 per data supplement. Many papers that describe the immune system, blood cells or blood vessels need to show histology or immunofluorescence images, which are usually presented in color. A hypothetical average length paper of 8 pages with four color images and one data supplement would cost the author: (8x$62) + (4x$620) +$105 = $3081. In addition to collecting this fee from the authors, the journal also then collects annual subscription fees from its readers, which are either $975 for an individual in the US, $1,220 for subscribers outside theUS and altogether much higher for a site license granted to a university library. Needless to say, these subscription fees are quite high and especially difficult to pay for in underdeveloped countries.

This $3,081 fee for a typical Blood paper has to be compared with the fees of the open access PLOS journals, which charge authors of PLOS One papers a flat fee of $1,350 (no matter how many color figures or supplements are used). The more prestigious PLOS Medicine and PLOS Biology journals charge a higher flat-fee of $2,900 per published papers. What is quite remarkable is that authors submitting to PLOS from underdeveloped countries pay either no author fees or a nominal $500 fee, depending on which country they are submitting from. Due to the open access nature of the PLOS journals, anybody can access the articles without having to pay any subscription or access fees, which is especially helpful to researchers in countries with minimal financial resources for education and research. PLOS journals are published by a non-profit organization, so this may explain why they are able to offer such affordable prices to authors and free access to all readers. However, even the recently founded open access journal Scientific Reports published by the Nature Publishing Group only charges $1,350 to the authors.

Science was never meant to be conducted by the rich for the rich. The goal of scientists should be to communicate rigorous findings to as broad an audience as possible. Open access publishing is a step in the right direction, because it helps liberate the scientific enterprise from corporate interests of pay-for-access publishers that impair the broad dissemination of scientific knowledge to readers who cannot afford the high subscription fees.

4. Specific responses to Dr. Fields

In this section, I will just highlight some of the statements made by Dr. Fields that I disagree with and give brief responses:

“Scientific publication is undergoing a drastic transformation as it passes deeper into government and capitalistic control, while weakened from struggling simultaneously to cope with unprecedented transformations brought about by electronic publication.”

“The federal government has mandated that scientific research that is funded in part by federal grants be made freely available to anyone over the Internet.”

Scientific publication is not passing into government and capitalistic control. It has always been under capitalistic control. The government mandates do not concern the publication itself (i.e. the government does not interfere with peer review and editorial decisions), but governments are pushing for free access to the publications. The electronic publication is not a weakening, but a strengthening because it facilitates rapid sharing and communication of scientific results.

“In the absence of income derived from subscriptions, scientific journals must now obtain the necessary funds for publication by charging the authors directly to publish their scientific study. The cost to authors ranges from $1,000 to $3,000 or more per article. Scientists must publish several articles a year, so these costs are substantial.

The funding model fueling open-access publication is a modern rendition of the well-known “vanity” model of publication, in which the author pays to have his or her work printed. The same well-appreciated negative consequences result when applied to scientific publication. Because the income is derived from the authors rather than from readers, the incentive for the publisher is to publish as much as possible, rather than being motivated by a primary concern for quality and significance that would increase subscription by readers, libraries and institutions and thus income. In the open-access, “author-pays” financial model, the more articles that are published, the more income the publishers collect.”

Dr. Fields is referring to the charges of open access journals, but he does not mention that the authors also have to pay substantial fees to traditional pay-for-access journals to have their work published. These charges are at times even higher than those of open access journals especially when researchers use color figures, which is common in research areas that rely heavily on fluorescence imaging (see example above for the journal Blood). It is true that more articles may generate more profits for some open access publishers, but this is where the quality of the peer review process and editorial policies of a journal need to be evaluated. The open access PLOS journals are run by a non-profit organization and have no need to generate more profits. The problem pointed out by Dr. Fields applies to all for-profit publishing – whether it is open access or traditional pay-for-access. The best remedy is to ensure that the peer review process and editorial decisions are made by people who have no conflict of interest with the financial goals of the publishers.

“In place of rigorous peer review and editorial oversight by the leading scientists in the field, these publishers are substituting “innovative” approaches to review submissions, or they apply no authoritative review at all. Some open-access journals ask reviewers to evaluate only whether the techniques used in the study are valid, rather than judging the significance or novelty of the findings.”

Open access journals such as PLOS or eLife do have rigorous peer review in place and editorial oversight by some of the leading scientists in the field. There may be some open access journals which are not peer reviewed, but there are also pay-for-access journals that publish papers with minimal or no peer review. It is true that some open access journals such as PLOS One want reviewers to focus on the scientific validity of the research instead of whether or not it the research is deemed to be significant. This has advantages and disadvantages. By focusing on the validity instead of the significance, rigorous science gets to be published, independent of whether or not the area of research is “popular”. It also allows for the publication of studies that attempt to replicate previous work, instead of only focusing on new developments. The disadvantage is that a journal may publish multiple studies that merely re-affirm established scientific concepts or work on obscure species that are of no interest to the mainstream. On balance, I think it is a positive development, because I think that current journals under-emphasize the importance of replicating biomedical research and because I think that sometimes the “insignificant” areas of research may give rise to very new concepts that the mainstream of science would have otherwise ignored.

“The argument is made that the loss of rigorous scrutiny and validation provided by the traditional subscription-based mechanism of scientific publication will be replaced by the success of an article in the market after it is published — it’s the “cream-will-rise-to-the-top” theory.”

“Now when a scientist writes up new research for publication in a prestigious journal, he or she must deal with all the contradictory findings of questionable rigor and accuracy being published by these vanity-publishing, open-access journals.”

As mentioned above, open access journals such as the PLOS family do have rigorous scrutiny. The open access allows for an additional mechanism of scrutiny, by allowing readers all over the world to read the article, replicate it and in some cases also comment on the article in the form of a post-publication peer review.

The phrase “vanity-publishing, open access journals” is quite bizarre. There are prestigious open access journals such as PLOS Medicine, PLOS Biology and the newly emerging journal eLife and there are prestigious pay-for-access journals such as Nature or Cell. But there are also many not so prestigious pay-for-access journals that publish work of questionable rigor or significance.

“Similar changes are eroding literary publication as direct electronic publication by authors on the Internet has led to erotic and reportedly pornographic works like Fifty Shades of Grey and spinoffs sweeping bestsellers lists for months. The issue is not whether erotica or pornography is or should be popular; rather, one wonders what literary work might have filled those slots on the bestsellers lists if traditional mechanisms of editor-evaluated publication had been applied, which consider more than simply the potential popularity of a work in deciding what to publish.”

Responding to these assertions is again a daunting task. The preceding paragraph by Dr. Fields referred to “open access publishing” of scientific papers, but this paragraph now makes references to self-published erotica or pornography. I do not understand how peer-reviewed open access papers in journals such as PLOS One or PLOS Medicine are “similar” to self-published erotica or pornography. I have read published PLOS papers and I have been a peer reviewer for PLOS manuscripts prior to their publication and I can assure you that these open access scientific papers are not very erotic and not self-published. Open access scientific papers published in journals such as PLOS papers are free of charge, whereas even self-published erotica can require the payment of a fee. Erotica have been popular for as long as literature has been popular. Some of the great works of literature are erotica or have major erotic themes, so it is not clear to me why erotica and literary works are presented as being mutually exclusive. The “reportedly pornographic” phrase makes me wonder whether Dr. Fields has even read “Fifty Shades of Grey”. Neither have I, so I cannot comment on the quality of “Fifty Shades of Grey”, but I know that the book has received some pretty bad reviews. Its literary quality or lack thereof is not necessarily a function of being self-published. Many best-sellers released by established publishers are also routinely panned by literary critics. Furthermore, even famous authors such as Marcel Proust were occasionally forced to self-publish their works, because publishing houses did not think that the manuscripts were in keeping with moral standards or that they would have a high market value.

Self-publication is actually a platform to publish books that are rejected by traditional publishers who focus on profitability and marketability of books and are averse to taking risks. It is true that the loss of editorial review in self-published books can result in the publication of poor-quality books, but that is a function of poor writing and not of self-publication. Proust and others were able to produce literary masterpieces even though they used the self-publication route. Self-publication increases the volume of published books and articles and does put an increased burden on readers and reviewers to discriminate between “good” and “bad” work. This increased burden is off-set by the opportunity that self-publishing offers for innovative books that are not considered profitable or marketable by traditional publishers. However, open access scientific journals are not self-published. Therefore the discussion about self-published erotica in the context of open access scientific publications is an unnecessary and irrelevant distraction.

“Scientists and the public are rightfully outraged and we all suffer when flawed scientific studies are published. Even with the most rigorous review at the best journals, flawed studies sometimes slip through, such as the “discovery” of cold fusion published in Science, but it is the rarity of this lapse that makes this so sensational when it happens. With the new open-access model of author-financed publication, the “outstanding” is drowned in a flood of trivial or unsound work.”

We actually do not know much about how much flawed research is published in pay-for-access journals. The vast majority of retractions stem from pay-for-access journals and so far there is no evidence that open access publication is drowning out outstanding research.

“The logic for this government mandate is peculiar. Why do this to science? The scientific journals claim no rights to the results of publicly funded scientific research; they only seek financial compensation for the expenses required for editing, reviewing and producing the article to validate and disseminate the findings as effectively as possible.”

The huge profits made by academic publishers using the pay-for-access model, where they make authors pay submission fees and also generate huge revenues from subscriptions clearly contradicts that publishers are out to maximize their profits. The answer to “Why do this to science?” is simple: Science belongs to all humankind.

“One wonders how many new advances in science will never have an opportunity to take root now that scientific publication is an increasingly corporate and government business rather than the scholarly academic activity that it was for centuries.”

Dr. Fields again forgets to mention that scientific publication has been a corporate run business in the past. The government is mandating free access to scientific research results, not running a business on the side.

In summary, Dr. Fields article is a diatribe against both open access and digital publishing, but few, if any, of the arguments are convincing. Many scientists who support both digital publishing and open access have great expectations for how it will help improve science. We think that digital publishing saves time and allows us to invest this time into conducting and analyzing research. Open access enables us to share scientific results with thousands and perhaps millions of students and scientists all across the globe. Scientific and medical developments published in open access journals are instantaneously available to everyone, whether it is scientists in Germany, patients in the USA or biology teachers in Mali. This allows everyone to partake in the scientific enterprise either by implementing the research findings or by enabling them to intellectually contribute to science. These are the reasons why science will improve in the new era of scientific publication. Even though we have great expectations, we also know that there will be many obstacles along the way. We have to continuously reevaluate the shift to open access publishing and we need objective and constructive criticism instead of rants to ensure that the new era of scientific publications maintains or even improves the quality of science that is published.